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Institut de Biologie StructuraleGrenoble / France

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Welcome to the solid-state NMR and dynamics team.


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Solid-state NMR and dynamics team.

Permanent team members Beate Bersch and Paul Schanda.

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Our research focus : Understanding the motion of proteins at atomic resolution and the link to molecular function

Understanding protein function at atomic level requires the characterization of protein structure, dynamics and interaction at atomic resolution. While the knowledge of the three-dimensional structures of biomolecules is an important step towards this understanding, many interesting biomolecular processes require that biomolecules dynamically explore a range of different conformational states.

Our main research interest is the characterization of proteins that rely on motion to perform their function. In particular, we are interested in understanding the mechanisms by which membrane proteins transport metabolites through the phospholipid bilayer, and furthermore the modes of action of chaperones interacting with aggregation-prone molecules. We use Nuclear Magnetic Resonance spectroscopy, both in the solid-state and in solution-state to probe structure interactions and dynamics in these systems. In parallel and complementary to these studies of biomolecular function, we actively develop and improve NMR techniques, in particular solid-state NMR approaches, which provide insight into biomolecular dynamics at increasing level of detail.
Read more in the Research section

NEWS

Webinar about Molecular chaperones

An exciting webinar is upcoming, on Sept 9+10, 2020. Check the details at the Protein Society Webpage

A recent presentation of some of our solid-state NMR work is online :

(Starting at about 43 minutes)

Integrated structure determination of a 0.5 MDa enzyme complex by NMR and EM


In a great team effort, together with the cryo-EM team at IBS, and collaborators in Frankfurt and at NIH, we have recently set a new record for protein structure determination by NMR, combined with cryo-EM, by determining the structure of the dodecameric (12 x 39 kDa) aminopeptidase TET2.

The approach hinges on the availability of secondary structure from solid-state NMR, distance restraints, equally primarily from solid-state NMR, a cryo-EM map, and a clever approach that we developed, with Diego Gauto and Adrien Favier.
The resonance assignment, at that point the largest protein assigned, has been achieved with high-dimensional solid-state NMR, without the need for any fancy labeling, and the distance measurements combined methyl labeling, allowing the simultaneous detection of through-space proximities between methyls and backbone amides.

The approach opens new avenues for determining structures of large proteins by solid-state NMR.

Gauto et al. & Schanda, bioRxiv 2018 and Nat. Commun. 2019

Congratulations Diego, Adrien, Leandro and all the team for this great breakthrough !

Detailed insight into the motion of a 468 kDa-large enzyme complex : zoom on aromatic ring motions


NMR is able to decipher minute details of protein motion - and link them to function, and to fundamental aspects of their structural and mechanistic properties.

Bringing together advanced isotope labeling (together with Masatsune Kainosho & Roman Lichtenecker), and solid-state NMR, we have recently resolved the motions of phenylalanines in a large enzyme assembly at great detail. Do the aromatic residues undergo reorientations, known as "ring flips" ? On which time scale ? And how are those dependent on the structural context ?

Our recent study sheds light on these questions, and also reveals how a protein "unfreezes", by following phenylalanine motions from -170 degrees C to room temperature !

Read the whole story here Gauto et al & Schanda, JACS 2019

Online webinar highlighting solid-state NMR work from our group

In the context of the International Conference on Magnetic Resonance in Biological Systems, Paul recently presented work on the use of NMR, cryo-EM and MD to resolve structure, dynamics and function of protein assemblies. The talk is available on Youtube

New insights into membrane protein import into mitochondria.

Membrane proteins are highly aggregation prone in aqueous solution, but many of them need to be translocated across water-filled cellular compartments. This is particularly the case for membrane proteins working in mitochondria, the "power houses" of our cells. We have two recent papers/preprints out. In a first study, together with our colleagues in Freiburg, we revealed how a class of membrane proteins with three trans-membrane helices, the ’pyruvate carriers’, are imported into mitochondria.

Very recently, we furthermore resolved the subunit dynamics of the central chaperone family in the mitochondrial inter-membrane space, known as ’small TIMs’, and we deciphered the structure of a yet unresolved chaperone, TIM9·10·12, published as a preprint in bioRxiv.

Kathi’s paper on mitochondrial chaperones is featuring on the cover of Cell.

How can the highly aggregation-prone membrane proteins be transported across aqueous cellular compartments ? Read our story HERE and a press release from our colleagues in Freiburg HERE

How does the crystal packing influence protein dynamics ?

Crystallography is based on the inherent assumption that the crystal has only minor effects on the protein, but how well justified is this assumption ? Do proteins undergo the same types of motions in solution and in crystals ? Are proteins able to undergo slow conformational changes involving the simultaneous reorientation of groups of residues ? And is the time scale of such motions altered by the crystal packing ? And do the protein molecules as a whole undergo overall-motions ?
In our latest study we answer these questions in detail, using three different crystal forms of the same molecule. We show that both the local and the global motion differ in different crystal lattices. Find more in the paper

Native nanodiscs as a tool for membrane protein studies


Atomic-resolution studies of membrane proteins generally suffer from the need to extract the protein from its native lipid environment, which can introduce perturbations of structure and dynamics. We show that the use of a polymer allows to extract directly a patch of native membrane with the protein embedded, and this type of native nanodiscs enable high-resolution solid-state NMR studies, opening possibilities for probing structure, interactions and dynamics of membrane proteins in a near-native environment.
Find out more : Bersch et al, "Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion Facilitator Protein in Native Nanodiscs"

Sensitive solid-state NMR of large proteins through methyl labeling


Studying very large protein complexes is enabled by selective methyl labeling. We recently showed that CH3 labeling provides highly sensitive spectra of protein assemblies from several hundred kilodaltons to a megadalton.
Read paper Kurauskas et al, "Sensitive proton-detected solid-state NMR spectroscopy of large proteins with selective CH3 labelling : application to the 50S ribosome subunit"

Key words : Protein dynamics and mechanisms * Macromolecular machines * Methods development
Mots clés : Dynamique des protéines et mécanismes * Nanomachines macromoléculaires * Développements méthodologiques

Collaborations :

Molecular Dynamics simulations :
* Kresten Lindorff-Larsen (Univ. Copenhagen)
* Christophe Chipot and Francois Dehez (Univ. Nancy)
* Nikolai Skrynnikov (Purdue University)

Mitochondrial membrane proteins and import into mitochondria :
* Eva Pebay-Peyroula (IBS Grenoble)
* Nils Wiedemann (Univ. Freiburg)
* Doron Rapaport (Univ. Tuebingen)

Integrated structural biology techniques :
* Guy Schoehn, Leandro Estrozi, Greg Effantin (IBS Grenoble)
* Martha Brennich (EMBL Grenoble)
* Jacques-Philippe Colletier (IBS Grenoble)